Anti-Brexit protesters in Westminster on the day of a debate on extending article 50.
Photograph: Kirsty O’Connor/PA

Labour will order its MPs to refuse to back an amendment on a second referendum, in a vote likely to see mass abstentions of MPs supporting a people’s vote who fear it is too soon for a fresh poll to win a parliamentary majority.

The Speaker of the Commons, John Bercow, unexpectedly selected a second referendum amendment from Sarah Wollaston, the former Tory MP who recently defected to the Independent Group (TIG), and who has won support from the Liberal Democrats for her amendment.

Labour sources immediately indicated, despite the party’s policy to back a second referendum, that it would instead order MPs to abstain because they disagreed with the timing of the vote.

Keir Starmer, the shadow Brexit secretary, told the Commons: “We are supportive of the principle, but it’s a question of timing.”

Senior Labour sources said they were highly suspicious of the motives of TIG in putting their amendment to the vote, and said they believed some were backing it in order to expose Labour tensions.

Labour MPs who are opposed to a second referendum also enthusiastically backed the opportunity to hold a vote in parliament on the measure, with one MP saying it would “lance the boil” and prove there was no support for a second referendum in parliament.

Caroline Flint, a Labour MP opposed to a second referendum, said she was “really delighted” that Bercow had selected the amendment because she would have the opportunity to vote against it.

The abstentions mean the amendment is likely to be heavily defeated. Labour MPs who are leading supporters of the People’s Vote campaign said they were supportive of abstentions and said they did not back putting a second referendum to a vote in parliament before it could win majority support.

One influential MP who called for People’s Vote supporters to abstain on the motion was Phil Wilson, the Labour MP for Sedgefield, who has devised a different strategy for obtaining a referendum with fellow Labour MP Peter Kyle, by offering an amendment at the next meaningful vote to back Theresa May’s deal in exchange for a referendum.

“Other opposition parties and groupings may have their reasons for putting down an amendment on a people’s vote, but I will be abstaining today ,” he said.

Alastair Campbell, a leading figure in the People’s Vote campaign, said it was “wrong to press a people’s vote amendment today when the issue is [article 50] extension”.

He said a second referendum was “a possible solution to the current crisis, not an option within it” and that there would be more opportunities ahead when other options to solve the Brexit crisis had been exhausted.

More than a dozen Labour MPs likely to vote against a second referendum include Gareth Snell, Denis Skinner, Kate Hoey and John Mann, who had earlier supported an anti-second referendum amendment that Bercow chose not to select.

The amendment with the best chance of passing is the backbenchers’ proposal submitted by Labour’s Hilary Benn and supported by his fellow Labour MP Yvette Cooper plus seven others including the Conservatives Oliver Letwin and Dominic Grieve.

The amendment says it is designed “to enable the House of Commons to find a way forward that can command majority support” by effectively allowing MPs to wrest control of parliamentary time from May’s government.

MPs' amendments for the Brexit article 50 extension vote

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A debate on Wednesday would allow the Commons to decide whether to hold a series of indicative votes to find which Brexit approach would command a majority in the house. It is also supported by SNP, Liberal Democrat and Plaid Cymru MPs.

The amendments are two of the four the Speaker has selected for Thursday evening’s vote on extending article 50. Voting is expected to start at about 5pm.

TIG MP Chris Leslie, who recently left Labour, tweeted: “So now we know it. Labour frontbench won’t support a people’s vote. Long suspected, now confirmed.”

A Labour frontbench amendment, chosen by the Bercow, instructs May to seek an unspecified extension to article 50 to avoid exiting the EU on 29 March without a deal and “to provide parliamentary time for this house to find a majority for a different approach.”.

That would imply a long extension as few believe a radically different Brexit deal to the one already negotiated by May can be agreed quickly with the EU.

The fourth amendment Bercow selected came from the Labour backbencher Chris Bryant, who wants MPs to vote on whether they believe May can put an unchanged Brexit deal before the Commons to a vote.

Parliamentary precedent holds that the government cannot ask MPs to vote twice on the same issue during the same session of parliament, to prevent the executive bullying the Commons by putting the same measure to a vote repeatedly.